Ruben Abagyan

Publications (3)38.15 Total impact

• Source

  Available from: ucl.ac.uk

  Article: Algorithms for high-density oligonucleotide array.

  Yingyao Zhou, Ruben Abagyan
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  ABSTRACT: As a global gene expression-monitoring tool, high-density oligonucleotide arrays (HDAs), accelerate biological and drug discovery processes. Computational considerations affect several key issues, from array design and accurate gene expression level determination to various aspects of the biological analysis of cell functions and gene networks. This review highlights recent progress in ideas and algorithms that are specific to HDAs. Replacing a large number of specific 'mismatch' oligonucleotides by a small number of general noise control oligonucleotides and using dynamic probe-to-gene mapping were some of the ideas proposed. Several novel mismatch-free probe-to-gene condensation algorithms have demonstrated the ability to take advantage of such designs, and provide higher density and equivalent or better calculation accuracy than previous algorithms. Algorithms to be developed in the future should significantly increase both the quality and quantity of information revealed by a single array; therefore, a single array containing the whole mammalian genome or even multiple genomes could soon become a standard tool.
  Current opinion in drug discovery & development 06/2003; 6(3):339-45. · 4.20 Impact Factor
• Source

  Available from: Karine G Le Roch

  Article: Excess polymorphisms in genes for membrane proteins in Plasmodium falciparum.

  Sarah K Volkman, Daniel L Hartl, Dyann F Wirth, Kaare M Nielsen, Mehee Choi, Serge Batalov, Yingyao Zhou, David Plouffe, Karine G Le Roch, Ruben Abagyan, Elizabeth A Winzeler
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  ABSTRACT: The detection of single-nucleotide polymorphisms in pathogenic microorganisms has normally been carried out by trial and error. Here we show that DNA hybridization with high-density oligonucleotide arrays provides rapid and convenient detection of single-nucleotide polymorphisms in Plasmodium falciparum, despite its exceptionally high adenine-thymine (AT) content (82%). A disproportionate number of polymorphisms are found in genes encoding proteins associated with the cell membrane. These genes are targets for only 22% of the oligonucleotide probes but account for 69% of the polymorphisms. Genetic variation is also enriched in subtelomeric regions, which account for 22% of the chromosome but 76% of the polymorphisms.
  Science 11/2002; 298(5591):216-8. · 31.20 Impact Factor
• Source

  Available from: PubMed Central

  Article: Match-only integral distribution (MOID) algorithm for high-density oligonucleotide array analysis.

  Yingyao Zhou, Ruben Abagyan
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  ABSTRACT: High-density oligonucleotide arrays have become a valuable tool for high-throughput gene expression profiling. Increasing the array information density and improving the analysis algorithms are two important computational research topics. A new algorithm, Match-Only Integral Distribution (MOID), was developed to analyze high-density oligonucleotide arrays. Using known data from both spiking experiments and no-change experiments performed with Affymetrix GeneChip arrays, MOID and the Affymetrix algorithm implemented in Microarray Suite 4.0 (MAS4) were compared. While MOID gave similar performance to MAS4 in the spiking experiments, better performance was observed in the no-change experiments.MOID also provides a set of alternative statistical analysis tools to MAS4. There are two main features that distinguish MOID from MAS4. First, MOID uses continuous P values for the likelihood of gene presence, while MAS4 resorts to discrete absolute calls. Secondly, MOID uses heuristic confidence intervals for both gene expression levels and fold change values, while MAS4 categorizes the significance of gene expression level changes into discrete fold change calls. The results show that by using MOID, Affymetrix GeneChip arrays may need as little as ten probes per gene without compromising analysis accuracy.
  BMC Bioinformatics 02/2002; 3:3. · 2.75 Impact Factor